December 22, 2008

X chromosome diversity in Africans and non-Africans

From the paper:

The ratio of the tMRCA between chromosome X and the autosomes in West Africans, 0.763 ± 0.026, is consistent with the expected 3/4, but it is lower than 3/4 in non-African populations: 0.635 ± 0.024 in North Europeans and 0.613 ± 0.026 in East Asians (Table 2, Supplementary Note and Supplementary Table 2 online).

I am fairly allergic to explanations invoking genetic drift, and I think that both selection and demography might play a role in the observed discrepancy.

Nature Genetics doi:10.1038/ng.303

Accelerated genetic drift on chromosome X during the human dispersal out of Africa

Alon Keinan et al.

Abstract

Comparisons of chromosome X and the autosomes can illuminate differences in the histories of males and females as well as shed light on the forces of natural selection. We compared the patterns of variation in these parts of the genome using two datasets that we assembled for this study that are both genomic in scale. Three independent analyses show that around the time of the dispersal of modern humans out of Africa, chromosome X experienced much more genetic drift than is expected from the pattern on the autosomes. This is not predicted by known episodes of demographic history, and we found no similar patterns associated with the dispersals into East Asia and Europe. We conclude that a sex-biased process that reduced the female effective population size, or an episode of natural selection unusually affecting chromosome X, was associated with the founding of non-African populations.

I wonder if in extremely violent or war-like cultures, you wouldn't get genetic data that looked like the footprint of polyandry simply because so many men die before being able to father multiple children by the same woman.

Hello. This raises for me a question much on my mind as I look to sort out what all these articles mean. The question is, to what degree are mini extinction events taken into account in calculating relative diversity. Example: Otzi was reported to be of a different configuration of mtDNA than has yet been found in the region. I look at the 10,000 or so bodies in the mass grave in the Greek region of Sicily and wonder if those COULD be typed, would there be groups among them no longer among us. Especially considering the Black Death, WWI, WWII and the impact of the Ice Age on those groups living in Europe at the time, I think this has to be a much larger factor in the equation than I have yet seen reflected in articles. But that maybe is the measure of MY ignorance.

John: abslutely yes. Though you don't really need to look for bottlenecks that are not such thing (even the black death did not cause enough casualties as to be considered a bottleneck, properly speaking). Mere drift will cause some clades to vanish and others to expand randomly all the time. Smaller clades are, of course, more likely to succumb in the process.

But there may be other reasons: if some mtDNA clades, for example, carry a deletereous mutation (as does happen), they won't surely survive for too many generations. In fact all deletereous mutations found in extant mtDNA are at the very end of the tree, in newly sprung branches that are not likely to survive in the mid run. Inversely, though the examples are less clear, there could be some clades that give some marked advantage (greater fertility, improved constitution...) and these would be more likely to get consolidated in the mid-run - ceteris paribus.

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